[Chimera-users] How to place a metal ion in protein model

[Elaine Meng]

Hi Suneel,
The UniProt fetch is fairly new, you would need to get a recent daily build:
<http://www.cgl.ucsf.edu/chimera/download.html#daily>
<http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html>

In older (but not too old) versions another approach is to get a file of the sequence in fasta format, then open it with "File... Open" in the Chimera menu.

If you get a newer Chimera and still have the modelling error, please use "Help... Report a Bug" in the menu to report it -- it will include information on your computer and what version you are using.  This chimera-users email address is mainly for questions, not bugreports.  Thanks!

There are explanations of how to superimpose structures (such as your template and model to see where the metal site would be) here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

Good luck,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 5, 2012, at 2:00 PM, Suneel N.A. wrote:

> Hi Elaine
> Thank you very much for the timely reply. I am glad to see it. The information you sent was really helpful. Here are some of the details for your suggestions/queries
> (a) I used 1ZWX for homology modelling. The other closest models are 2DDR and 3I5V. They are crystallised with bound metal ions.As you suggested I will try to superimpose with the metal ion (though I am not that good in using chimera).
>  
> I have  another query: I am trying to model a protein based on homology modelling strategy. I came to know that Chimera can model the protein based on the same strategy. When I attempted modelling using the Modeller tool of chimera it gives me an error "Running modeller for  query via web service failed; see reply log for more information. When I see the reply log : Import modeller, Import error:No module named modeller".
> Infact I even got the licence key from the modeller website and used it in the dialogue box but still this error message is shown.
>  
> Another query is, for modelling a protein (whose structure is unknown) , how do we import the sequences into  chimera? In one of the chimera videos on modelling, they show that the protein sequence is  imported/fetched from Uniport. But in my  chimera software under the Fetch tab I don't see an Uniprot option. In this regard please tell me how to import sequences.
>  
> Please do the needful. Will be looking for the reply.
> Thanking you in anticipation
> Yours Sincerely
> suneel
>